I originally started out with the Kindle DX. Really liked it. However, I didn't like the fact that it was an 'e-ink' display that required external lighting. I read a lot, and most of the time during the evening at a cafe or restaurant (where a lot of times they dim the lighting to enhance the 'atmosphere'). I also didn't care for being stuck with hardware buttons to turn pages - made it difficult to find a good orientation in a book stand). Both of these reasons were why I decided to get an iPad. Being able to read in any lighting environment has made the purchase of the iPad completely worth while. It's made all the difference in the world.
Regarding the Kindle and iBook applications: They both have their pluses and minuses.
Kindle Pros:
~ Ability to configure landscape mode for single page viewing (cannot be done in iBooks)
~ Better font size scaling. In truth, it's not better, it's that it has the particular font size that I prefer - iBooks fonts are either too small or too large for me.
~ Better distribution of Amazon/Kindle books. You can have Kindle readers for Apple, PC, or Android devices (iBooks limited to Apple products)
~ Ability to sort library by most recently opened (cannot be done in iBooks)
~ Ability to zoom in on embedded graphics (cannot be done in iBooks).
Kindle Cons:
~ Inability to configure left margin tap for page advancement (can be done in iBooks)
~ Brightness adjustment bar defaulted too far into the 'bright' side - making it difficult to adjust brighter (iBooks has the opposite problem)
~ Limited to Amazon's propriety ebook format ( not necessarily limited, but it cannot read the more popular epub format - which is pure silliness from a marketing standpoint).
~ Cannot organize books into separate 'collections' (can be done in iBooks)
iBook Pros:
~ Better personal configurations - I can set it so that a tap on the left margin will advance the page (cannot be done in Kindle).
~ Can read the most common ebook formats (in truth, I only use iBooks to read epub format books that I obtain outside of Amazon).
~ Ability to organize books into separate collections (pseudo sub-folders).
iBook Cons:
~ Inability to configure landscape viewing to single page (can be done with Kindle) - this is something I really dislike.
~ Brightness setting always defaults to the dimmer end of the spectrum bar - difficult to fine-tune brightness to lower levels.
~ Font sizes too far apart - needs more levels of size adjustment (it's either too large or too small).
~ Inability to zoom in on embedded graphics (which often get cut off on their edges if their resolution is too large for the page size).
I think that overall, I prefer the Kindle Application. However, I'm forced to have to use the iBooks app when I have an e-book that I did not purchase/obtain from Amazon. I can however, use either one with ease - though when switching between the two, I have to re-train myself when I'm accustomed to tapping on the left margin to advance the page. I think that if the kindle app was modified so that it could be used to read non-Amazon books and have the left margin tap, page advance feature, it would be pretty much perfect for my purposes. I really like the left margin tap feature, as I often read while I'm eating, and most often I change pages with my left hand (the right hand being used to stuff food into my face). Because of this, I hate having to do the page swipe motion in the middle of the screen, as oftentimes my fingers are a bit greasy from my food...
Although I have the Nook application loaded on my iPad, I have never really used it - so I haven't formed any opinions either for or against it.